foldseek-structural-search

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://search.foldseek.com/search and https://github.com/steineggerlab/foldseek, then (2) create the file recording the notification text and timestamp.

Goal

Submit a user-provided 3D protein structure file (.cif, .mmcif, or .pdb) to the Foldseek web server API to find structurally similar proteins. Report the top structural hits, interpret key alignment metrics, summarize the inferred protein functions, save the Markdown-formatted table to a .md file, and save the full detailed results to a local JSON file.

Core Rules